muck: Calculate the amount of muck/contamination to explain an observed C14 age

Description

Given an observed and a target radiocarbon age, calculate the amount of contamination required to explain the observed age.

Usage

muck(
  y.obs,
  y.obs.er = 0,
  y.target,
  y.target.er = 0,
  F.contam = 1,
  F.contam.er = 0,
  MC = TRUE,
  its = 10000,
  roundby = 1,
  decimals = 3,
  visualise = TRUE,
  talk = TRUE,
  eq.x = 5,
  eq.y = c(),
  eq.size = 0.8,
  target.col = "darkgreen",
  observed.col = "blue",
  contamination.col = "red",
  target.pch = 20,
  observed.pch = 18,
  contamination.pch = 17,
  true.name = "target",
  xlab = "contamination (%)",
  ylab = "F14C",
  ylim = c(),
  C14.axis = TRUE,
  bty = "u"
)

Value

The required contamination (as percentage), as well as a plot

Arguments

y.obs: The observed radiocarbon age
y.obs.er: The error of the observed radiocarbon age
y.target: the target radiocarbon age
y.target.er: The error of the target radiocarbon age. Not taken into account in the calculations.
F.contam: the F14C of the contamination. Set at 1 for carbon of modern radiocarbon age, at 0 for 14C-free carbon, or anywhere inbetween.
F.contam.er: The error of the contamination. Defaults to 0.
MC: Whether or not to use Monte Carlo iterations to estimate the values. Defaults to TRUE, because it treats uncertainties better than if set to FALSE.
its: Amount of iterations to use if MC=TRUE. Defaults to 10,000.
roundby: Rounding of the output for C14 ages. Defaults to 1 decimal.
decimals: Rounding of the output. Since details matter here, the default is to provide 5 decimals.
visualise: By default, a plot is made to visualise the target and observed F14C values, together with the inferred contamination.
talk: Whether or not to report the calculations made. Defaults to talk=TRUE.
eq.x: Leftmost location of the equation. Defaults to eq.x=5. Can be set to values outside of (0,100) to make the equation invisible.
eq.y: Vertical location of the equation. Defaults to the top of the graph.
eq.size: Size of the font of the equation. In case the equation gets jumbled up upon resizing of a graphical device, just issue the previous `clean` command again. Defaults to eq.size=0.8.
target.col: Colour for the target/true values. Defaults to darkgreen.
observed.col: Colour for the observed values. Defaults to blue.
contamination.col: Colour for the contamination values. Defaults to red.
target.pch: Icon for the target. Defaults to a filled circle.
observed.pch: Icon for the observed. Defaults to a diamond
contamination.pch: Icon for the contamination. Defaults to a triangle.
true.name: Name of the label of the true/target date
xlab: Name of the x-axis. Defaults to 'contamination (%)'.
ylab: Name of the y-axis. Defaults to 'F14C'.
ylim: Limits of the y-axis. Calculated automatically by default.
C14.axis: Whether or not to draw a secondary vertical axis for C14 ages. Defaults to C14.axis=TRUE.
bty: Draw a box around a box of a certain shape. Defaults to bty="u".

Author

Maarten Blaauw

Details

Whereas the function takes true/target and observed C14 ages as input and percentage contamination as output, internal calculations are done in the F14C realm and using contamination fractions (between 0 and 1). The central calculation is `frac = (F_obs - F_true) / (F_contam - F_true)`, where `frac` is the fraction of contamination to explain how we went from the observed to the true C14 age, `F_obs` is the observed C14 age in F14C, `F_true` is the true or target age in F14C, `F_contam` is the F value of the contamination. In some extreme cases (e.g., if dividing by zero), the calculation will spit out unexpected results. Messages will be provided in most of these cases.

Examples

Run this code

  muck(600, 30, 2000, 0, 1, .01)

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